Msgr. Silvio José Báez, with microphone, and Cardinal Leopoldo Brenes, left of him, addressed residents of Masaya, Nicaragua, last month. “An authentic pastor of the Catholic Church will never side with the executioners,” Monsignor Báez said.CreditCreditMarvin Recinos/Agence France-Presse — Getty Images

MANAGUA, Nicaragua — Nicaragua’s senior Catholic clergy linked arms and pressed through a hostile, pro-government crowd screaming “murderers.” As they reached the basilica with a dozen people trapped inside, some of the mob burst in behind them.

In the scuffle, somebody slashed Managua’s auxiliary bishop, Msgr. Silvio José Báez, in the arm and ripped the insignia from his cassock. Eventually, the shoving ended and the clerics brought out the group — paramedics and Franciscan missionaries who had sought safety from the crowd.

Monsignor Báez brushed off the assault.

“What the people are going through is much more serious,” he said to reporters accompanying the clerics.

The Roman Catholic Church is on the front lines of an escalating conflict between the increasingly authoritarian government of President Daniel Ortega and the broad-based opposition that wants him gone. In a country where the church has often been immersed in politics, priests are both witnesses and players in the crisis that has racked the nation for the past three months and claimed almost 300 lives.

“We continue to be pastors, and an authentic pastor of the Catholic Church will never side with the executioners,” said Monsignor Báez. “He will always be with the victims.”

In the first days of the upheaval, Mr. Ortega appealed to the bishops to act as mediators in talks with the opposition, an alliance of disparate groups including students, business associations and farmers’ organizations. But as the government intensified its crackdown on the opposition, Mr. Ortega has stopped treating the bishops as neutral arbiters, unleashing attacks by his followers on priests and on churches.

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Police officers blocked the entrance to the Church of Jesus of the Divine Mercy in Managua this month. Pro-government paramilitaries laid siege to the church during a night of gunfire.CreditOswaldo Rivas/Reuters

The government “has declared war on the church,” said Juan Sebastián Chamorro, a member of the opposition alliance.

While the church tried to strike the delicate balance between mediator and defender, it was Monsignor Báez who emerged as the face of the opposition, with a commanding presence over social media. The role gives him the freedom to denounce the government without reservations.

“What there is here is an armed state against an unarmed people,” he said in an interview at the seminary where he lives on the outskirts of Managua. “This is not a civil war.”

On the streets, the church defends the rebellion’s foot soldiers, including the citizens who guarded cobblestone barricades to hold their neighborhoods against Nicaragua’s national police and their paramilitary enforcers.

Monsignor Báez, 60, argued that there was no contradiction between the two tasks.

“One thing that has to be clear is that being the mediators of a dialogue does not make us neutral before injustice, before human rights violations, before the death of innocents,” he said.

The government’s campaign against the protesters became more forceful in the past couple of weeks, timed to last Thursday’s anniversary of the 1979 Sandinista Revolution that first brought Mr. Ortega to power. Almost every day, convoys of Toyota trucks crammed with masked paramilitaries rolled into the rebellious towns south of Managua to demolish the barricades.

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Carrying a coffin with the body of a protester shot during a clash with pro-government forces in Masaya, Nicaragua.CreditCristobal Venegas/Associated Press

Protesters die daily, and many more have been injured and arrested as the resistance hardens against the rule of Mr. Ortega and his wife, Vice President Rosario Murillo. Most of the dead were civilians, some teenagers — but police officers have also been killed.

Now the priests themselves have become targets. Mr. Ortega devoted much of his speech on Thursday to an angry denunciation of the church, accusing the bishops of working to overthrow his elected government and even of using some churches to hide arms.

“I thought they were mediators, but no,” he said. “They were committed to the coup-plotters, they were part of the plan with the coup-plotters.”

He has refused a proposal by the bishops to move up the 2021 elections to next year, and has branded the opposition as terrorists.

The attacks on the church have been building since Mr. Ortega first condemned “those who curse us and condemn us to death in the name of religious institutions” a couple of weeks ago.

Two days later, Monsignor Báez, along with the Managua archbishop, Cardinal Leopoldo Brenes, and the papal nuncio, Monsignor Waldemar Sommertag, answered the call to rescue a group of Franciscan missionaries and paramedics trapped in the basilica in Diriamba, an hour south of the capital, and ran into the angry mob.

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President Daniel Ortega, right, in Managua this month. He denounced “those who curse us and condemn us to death in the name of religious institutions.”CreditAlfredo Zuniga/Associated Press

Then, paramilitaries laid siege to a church at the edge of the main university campus in Managua after attacking and expelling the students who had occupied the campus for two months. The students who took shelter in the Church of Jesus of the Divine Mercy along with priests and journalists endured a night of gunfire until the bishops won their release at daybreak.

“Government of Nicaragua crosses the limit” of the “inhuman and immoral,” Monsignor Báez wrote on Twitter in Spanish, English and Italian, ending with a plea: “The international community cannot be indifferent!”

In a pastoral letter the following day, the bishops added their frustration to Monsignor Báez’s rage, declaring that the government had shown no political will in negotiations because it refused to address any of the proposals intended to advance democracy.

The government’s representatives, the bishops wrote, “have distorted the principal objective for which the national dialogue was set up.”

The dual role between mediator and protector puts the church in a delicate position in the dialogue between the government and the opposition aimed at finding a peaceful transition, said Jaime Wheelock, who was a revolutionary commander alongside Mr. Ortega.

Mr. Wheelock supports the church’s role in the dialogue, but he warned that Mr. Ortega could decide that the church is “not a constuctive mediator.”

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Student protesters being welcomed by family and friends after emerging from an hourslong siege by pro-government forces.CreditJorge Torres/EPA, via Shutterstock

But María López Vigil, a former nun who writes frequently about the Nicaraguan church, said there is a growing acknowledgment that the priests — many of whom have received death threats — are risking their lives in the name of democracy.

“They pray for us. They intercede for us,” said María José Téllez Flores, 34, after Monsignor Báez and Cardinal Brenes spoke last month in the town of Masaya. “We have the confidence that they will support us.”

The church’s involvement in Nicaraguan politics is a tangled story that goes back decades. The conservative church hierarchy condemned the Somoza dictatorship, but was reluctant at first to embrace the Sandinistas.

By the spring of 1979, the bishops issued a pastoral letter denouncing the Somoza dictatorship as a tyranny and in July, when the Sandinistas converged in Managua, Archbishop Miguel Obando y Bravo offered a Mass to welcome them.

But soon the archbishop and the church hierarchy turned against the new Sandinista government as its Marxist policies hardened. Pope John Paul II suspended four priests who had posts in the Sandinista government after they refused to step down.

Mr. Ortega’s rule through the 1980s was known for blackmailing and setting up Catholic priests in compromising positions. Archbishop Obando y Bravo became the face of Nicaragua’s civilian political opposition as the United States supported a military force against the Sandinistas.

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Members of Nicaragua's Special Forces in Masaya.CreditOswaldo Rivas/Reuters

After Mr. Ortega lost the presidential election in 1990 — and as he planned a route back to power — he moved closer to the Catholic Church.

In 2004, Mr. Ortega asked for forgiveness for Sandinista attacks on the church during the 1980s, and the following year Cardinal Obando y Bravo married Mr. Ortega and Ms. Murillo.

As the 2006 election approached, Mr. Ortega threw his support behind the church’s call for a total ban on abortion. With Sandinista support, the ban became law 10 days before the vote that returned Mr. Ortega to the presidency.

Once in office, Mr. Ortega began to dismantle all the checks and balances on his power, reshaping the judiciary, congress and the electoral institute to maintain his hold on power. In what most critics saw as a betrayal, Cardinal Obando y Bravo remained by his side until the cleric died last month.

“They had their church with Cardinal Obando y Bravo,” said the Rev. José Alberto Idiáquez, rector of the Jesuit Central American University in Managua. The cardinal “had an important role during the Sandinista guerrilla war” and the fight against Somoza, “but then he was at the service” of the presidential couple. “They didn’t need much from the current bishops,” Father Idiáquez said.

The rest of the church hierarchy went their own way, he added. In a letter to Mr. Ortega in 2014, the bishops warned that the concentration of power in his hands posed an alarming threat. “If you read that letter, it is valid today,” Father Idiáquez said.

Monsignor Báez, a scholar of the Bible who returned to Nicaragua nine years ago from Rome after 30 years away, had another, more direct way of communicating: social media. What had initially been a way “to communicate reality from a Christian vision,” has taken on new urgency since the uprising, becoming a source of news and solace. It is also where Monsignor Báez has been fiercely criticized by dozens of pro-government accounts created after the crisis began.

If a priest tells him that a young person has been killed, “I send out the message and so it is not only the truth, but the testimony of the priest and my human solidarity at the same time,” Monsignor Báez said.

“My social media have made a terrible enemy of the government,” he said.

Correction:

An earlier version of this article referred imprecisely to comments made by Jaime Wheelock, who was a Sandinista commander in the 1979 revolution. While Mr. Wheelock suggested that the Ortega government might decide that the church is not a constructive mediator between the government and its opponents, Mr. Wheelock fully supports the church’s role in the dialogue and condemns the paramilitaries’ attacks on protesters.

A version of this article appears in print on , on Page A8 of the New York edition with the headline: Nicaragua Clergy, Siding With Protesters, Is Branded ‘Enemy’ of Ortega. Order Reprints | Today’s Paper | Subscribe